rs11865093

Variant names:

• chr16-57366837-G-A
• rs11865093

Your query was ambiguous. Multiple possible variants found:

• chr16-57366837-G-A
• chr16-57366837-G-C
• chr16-57366837-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.102 in 152,098 control chromosomes in the GnomAD database, including 2,416 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.10 (2416 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.78
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15546 AN: 151980 Hom.: 2412 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0354

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.0168

Gnomad SAS AF: 0.0357

Gnomad FIN AF: 0.00282

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00980

Gnomad OTH AF: 0.0636

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.102 AC: 15562 AN: 152098 Hom.: 2416 Cov.: 32 AF XY: 0.0988 AC XY: 7346 AN XY: 74362

African (AFR) AF: 0.335 AC: 13900 AN: 41450

American (AMR) AF: 0.0353 AC: 539 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00634 AC: 22 AN: 3472

East Asian (EAS) AF: 0.0169 AC: 87 AN: 5158

South Asian (SAS) AF: 0.0355 AC: 171 AN: 4820

European-Finnish (FIN) AF: 0.00282 AC: 30 AN: 10620

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00980 AC: 666 AN: 67976

Other (OTH) AF: 0.0663 AC: 140 AN: 2112

Alfa AF: 0.126 Hom.: 1020

Bravo AF: 0.114

Asia WGS AF: 0.0470 AC: 165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.24
DANN	Benign	0.75
PhyloP100		-2.8

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11865093; hg19: chr16-57400749;